NetBeans has a helpful (to me anyway!) feature under the "Views" menu, called "Synchronize Editor with Views". As the name suggests, toggling this on will cause the navigator view to jump straight to a file when it’s opened in the editor.
I generally prefer this to the normal "Ctrl+Shift+1" shortcut for manually jumping to a file. However, the downside is that after editing several files, your navigator tree is a mess of multiple open directories.
Eclipse has similar functionality, but it also has a "collapse all" button at the top of its navigator view… restoring things with a single click having to scroll around. Does NetBeans have any similar mechanism for collapsing open directories? Maybe a poorly-documented keyboard shortcut buried in there or something?
Unfortunately, after further digging on the NetBeans discussion forums and mailing lists, it seems that this functionality simply doesn’t exist. That’s a shame… hopefully they’ll add it in the future.